7JWK

Crystal Structure of Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH) from Mycoplasma genitalium with bound NAD

Experimental procedure

Experimental method	SINGLE WAVELENGTH
Source type	SYNCHROTRON
Source details	APS BEAMLINE 21-ID-F
Synchrotron site	APS
Beamline	21-ID-F
Temperature [K]	100
Detector technology	CCD
Collection date	2020-03-19
Detector	RAYONIX MX-300
Wavelength(s)	0.97872
Spacegroup name	P 21 21 21
Unit cell lengths	91.600, 94.170, 172.800
Unit cell angles	90.00, 90.00, 90.00

Refinement procedure

Resolution	45.430 - 2.200
R-factor	0.1608
Rwork	0.159
R-free	0.19660
Structure solution method	MOLECULAR REPLACEMENT
Starting model (for MR)	5vmt
RMSD bond length	0.007
RMSD bond angle	0.837
Data reduction software	XDS
Data scaling software	XSCALE
Phasing software	MoRDa
Refinement software	PHENIX (1.18.2-3874)

Data quality characteristics

	Overall	Inner shell	Outer shell
Low resolution limit [Å]	45.430	45.430	2.260
High resolution limit [Å]	2.200	9.840	2.200
Rmerge	0.081	0.057	0.576
Rmeas	0.087	0.063	0.620
Total number of observations	545819
Number of reflections	76513	952	5566
<I/σ(I)>	14.58	28.28	3.62
Completeness [%]	99.9	97.9	100
Redundancy	7.134	6.02	7.223
CC(1/2)	0.998	0.996	0.910

Crystallization Conditions

crystal ID	method	pH	temperature	details
1	VAPOR DIFFUSION, SITTING DROP	8.5	287	MygeA.00914.a.B2.PW38693 at 18 mg/ml incubated with 3 mM glycerol-3-phosphate and NAD, then mixed 1:1 with MorpheusII(f11): 10%(w/v) PEG 8K, 20%(w/v) 1,5-pentanediol, 0.1 M GlyGly/AMPD pH 8.5, 0.02 M of each xylitol, D-(--fructose, D-sorbitol, myo-inositol, L-rhamnose monohydrate. Tray: 312789f11. Puck: pvq3-6.